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I got the HER2, ER, PR status of BRCA patients from the BRCA TCGA publication supplementary: https://www.nature.com/articles/nature11412#supplementary-information filename: TCGA_Supplementary Tables 1-4.csv column: HER2_Final_Status But since it is from 2012, after some months, I downloaded the newer clinical data from cbioportal**: http://www.cbioportal.org/study?id=brca_tcga#clinical filename: data_bcr_clinical_data_patient.txt columns: IHC-Status, HER2 fish status However, I noticed that hundreds patients had different her2 status then they had in the old tcga publication: Barcode IHC-status(cbioportal) Her2 fish status (cbioportal) HER2_Final_Status(tcga publication) TCGA-A1-A0SH Equivocal Negative Negative TCGA-A2-A04U Negative Positive Negative TCGA-A2-A0T2 Negative Not Evaluated Negative TCGA-A8-A06R Positive Positive Equivocal At first, I thought there is a method to convert both ihc and fish statuses into one (final status). But I failed to find such method. In TCGA-A1-A0SH, it seems Fish is prefered. In TCGA-A2-A04U , it seems it is IHC. in TCGA-A8-A06R it is neither. **I verified that for those 4 patients, her2 status is consistent between cbioportal and current TCGA clinical files. (her2_fish_status, her2_status_by_ihc in clinical files) Thanks in advance, Maor

When I try to run `samtools mpileup` it expects to find the BAM index in the same folder as the BAM file with the extension ".bai". I'm not sure how I can expose the BAM index to a tool that assumes a certain file location for the index.

Hi! Which is the best way to get access to the expression of long non-coding RNAs? Is there any processed data (I have already checked on the case explorer) or I should reanalyze the raw data using something like Cufflinks?

SVS files are availble through the website: https://portal.gdc.cancer.gov/cases/9fe336a8-08a7-4fe7-bf45-afd6a8eb9c75 They are also available on the data portal as of May 21 2018: (same page, click on Files, it leads to data portal. You can see svs files for this case) However issue an API call to: https://cgc-datasets-api.sbgenomics.com/datasets/v0/tcga/cases/9FE336A8-08A7-4FE7-BF45-AFD6A8EB9C75/files No svs files are available.

Hi! I'm trying to download the diagnosis data to see if I can find some correlations with my gene of interest. In the Data browser I can see the Diagnosis Details but despite making subgroups for the data import I can't get those details in the metadata file. Is there any way to extract them? Thanks

I've joined today as a beta user and started a project, but once I do a query and pull up a list of files, I'm unable to highlight them either on the query map or the list of files in order to add them to my project for analysis. Is this a bug or am I doing something wrong? The help page indicates that I should be able to click on a path to highlight and add those files. Thanks!

HI there, I've noticed that some TCGA samples have multiple RNA-Seq BAM files, what would be the difference between the files? If it's convenient to use one over the other, what criteria should be used to select such file. Example: TCGA-STAD RNA-seq TCGA-BR-8368-01A-11R-2343-13_rnaseq.bam 14.5GB _1_TCGA-BR-8368-01A-11R-2343-13_rnaseq.bam 14.7GB Thanks, Franco